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    SCNM1 sodium channel modifier 1 [ Homo sapiens (human) ]

    Gene ID: 79005, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SCNM1provided by HGNC
    Official Full Name
    sodium channel modifier 1provided by HGNC
    Primary source
    HGNC:HGNC:23136
    See related
    Ensembl:ENSG00000163156 MIM:608095; AllianceGenome:HGNC:23136
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    OFD19
    Summary
    SCNM1 is a zinc finger protein and putative splicing factor. In mice, Scnm1 modifies phenotypic expression of Scn8a (MIM 600702) mutations (Buchner et al., 2003 [PubMed 12920299]).[supplied by OMIM, Oct 2009]
    Expression
    Ubiquitous expression in spleen (RPKM 7.6), lymph node (RPKM 7.6) and 25 other tissues See more
    Orthologs
    all
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    Genomic context

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    See SCNM1 in Genome Data Viewer
    Location:
    1q21.3
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (151166144..151170296)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (150289872..150294025)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (151138620..151142772)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:151104130-151104914 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1313 Neighboring gene semaphorin 6C Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1314 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1315 Neighboring gene TNFAIP8L2-SCNM1 readthrough Neighboring gene LysM domain containing 1 Neighboring gene TNF alpha induced protein 8 like 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:151137860-151138565 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:151138566-151139272 Neighboring gene tropomodulin 4 Neighboring gene vacuolar protein sorting 72 homolog Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1710 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1711 Neighboring gene uncharacterized LOC124904419 Neighboring gene phosphatidylinositol-4-phosphate 5-kinase type 1 alpha

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Mutations in SCNM1 cause orofaciodigital syndrome due to minor intron splicing defects affecting primary cilia. Iturrate A, et al. Am J Hum Genet, 2022 Oct 6. PMID 36084634, Free PMC Article
    2. SCNM1, a putative RNA splicing factor that modifies disease severity in mice. Buchner DA, et al. Science, 2003 Aug 15. PMID 12920299
    3. Evidence for a direct role of the disease modifier SCNM1 in splicing. Howell VM, et al. Hum Mol Genet, 2007 Oct 15. PMID 17656373
    4. Protein microarray analysis identifies human cellular prion protein interactors. Satoh J, et al. Neuropathol Appl Neurobiol, 2009 Feb. PMID 18482256
    5. A high-confidence interaction map identifies SIRT1 as a mediator of acetylation of USP22 and the SAGA coactivator complex. Armour SM, et al. Mol Cell Biol, 2013 Apr. PMID 23382074, Free PMC Article

    See all (30) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Mutations in SCNM1 cause orofaciodigital syndrome due to minor intron splicing defects affecting primary cilia.
      Title: Mutations in SCNM1 cause orofaciodigital syndrome due to minor intron splicing defects affecting primary cilia.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Orofaciodigital syndrome 19
    MedGen: C5774248 OMIM: 620107 GeneReviews: Not available
    		not available

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Readthrough TNFAIP8L2-SCNM1

    Readthrough gene: TNFAIP8L2-SCNM1, Included gene: TNFAIP8L2

    Homology

    Clone Names

    • MGC3180

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables enzyme binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in RNA splicing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in alternative mRNA splicing, via spliceosome ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in nuclear speck ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of spliceosomal complex IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    sodium channel modifier 1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001204856.2 → NP_001191785.1  sodium channel modifier 1 isoform 2

      See identical proteins and their annotated locations for NP_001191785.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in the 5' UTR, compared to variant 1. These differences causes translation initiation at a downstream AUG and result in an isoform (2) with a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AK056322, AL592424, AV718162
      UniProtKB/Swiss-Prot
      Q9BWG6
      Related
      ENSP00000357898.1, ENST00000368902.1
      Conserved Domains (2) summary
      pfam15803
      Location:9 → 35
      zf-SCNM1; Zinc-finger of sodium channel modifier 1
      pfam15805
      Location:148 → 193
      SCNM1_acidic; Acidic C-terminal region of sodium channel modifier 1 SCNM1

    2. NM_024041.4 → NP_076946.1  sodium channel modifier 1 isoform 1

      See identical proteins and their annotated locations for NP_076946.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AL592424
      Consensus CDS
      CCDS987.1
      UniProtKB/Swiss-Prot
      B4DWR1, Q5JR74, Q9BWG6
      Related
      ENSP00000357901.4, ENST00000368905.9
      Conserved Domains (2) summary
      pfam15803
      Location:44 → 70
      zf-SCNM1; Zinc-finger of sodium channel modifier 1
      pfam15805
      Location:183 → 228
      SCNM1_acidic; Acidic C-terminal region of sodium channel modifier 1 SCNM1

    RNA

    1. NR_037937.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK056322, AL592424, BU540926, CD103880

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      151166144..151170296
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      150289872..150294025
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001002234.1: Suppressed sequence

      Description
      NM_001002234.1: This RefSeq was permanently suppressed because currently there is not sufficient data to support this transcript.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BWG6.1 GenPept UniProtKB/Swiss-Prot:Q9BWG6

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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